Variant report

Variant	rs1241179
Chromosome Location	chr1:103322341-103322342
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1020918	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1031821	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10782911	0.86[ASN][1000 genomes]
rs11164630	0.81[CHB][hapmap];0.88[JPT][hapmap]
rs1241171	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1241181	0.88[LWK][hapmap];0.95[MKK][hapmap]
rs1241182	0.97[MKK][hapmap]
rs1241186	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1241187	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1241194	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1241196	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1241198	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1241199	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1241200	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1241201	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1241202	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1241205	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1241206	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1241207	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1241208	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1241209	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1261690	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1263061	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1270748	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1271798	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12722976	0.81[CHB][hapmap];0.93[JPT][hapmap]
rs12731405	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1463038	0.83[YRI][hapmap]
rs1463039	0.85[LWK][hapmap];0.83[YRI][hapmap]
rs1463048	0.88[JPT][hapmap]
rs1621055	0.87[YRI][hapmap]
rs1622838	0.83[YRI][hapmap]
rs1676486	0.84[CHB][hapmap];0.82[CHD][hapmap]
rs1676493	0.85[LWK][hapmap];0.83[YRI][hapmap]
rs1676494	0.83[YRI][hapmap]
rs1676498	0.83[YRI][hapmap]
rs1676499	0.82[YRI][hapmap]
rs1676500	0.83[YRI][hapmap]
rs1676501	0.85[YRI][hapmap]
rs1676507	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1676508	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1676510	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17127203	0.85[CHD][hapmap];0.87[GIH][hapmap]
rs1763342	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1763343	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1763345	0.83[YRI][hapmap]
rs1763346	0.83[YRI][hapmap]
rs1763348	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1763349	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1763359	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2169608	0.81[CHB][hapmap];0.88[JPT][hapmap]
rs2169609	0.81[CHB][hapmap];0.87[JPT][hapmap]
rs2169610	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2229783	0.81[CHB][hapmap];0.90[CHD][hapmap];0.88[JPT][hapmap]
rs2616002	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2783566	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2783570	0.88[LWK][hapmap]
rs4907983	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4908270	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61157885	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs644019	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs899019	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs899020	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs945326	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs9659030	0.85[CHD][hapmap]
rs969272	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830882	chr1:103192683-103355802	Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv522922	chr1:103305021-103764640	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1241179	SLC35A3	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:103318400-103324000	Weak transcription	Osteobl	bone
2	chr1:103318400-103324600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:103320600-103324000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:103321000-103322400	Weak transcription	Fetal Intestine Large	intestine
5	chr1:103322200-103323800	Weak transcription	NHDF-Ad	bronchial

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